University vice-chancellors are agitating for a delay in the deregulation of course fees, throwing the federal government's higher education reforms into disarray.

The university leaders fear as many as 160,000 school leavers nationwide could select a course without knowing whether they will be up for tens of thousands of dollars in extra fees, which some students would struggle to pay.

"The decision to remove the cap on fees in 2016 is premature": UWS vice chancellor Barney Glover. Photo: Gene Ramirez

University of Western Sydney vice-chancellor Barney Glover asked for the postponement of the planned fee deregulation during talks with the office of Education Minister Christopher Pyne last week.

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Professor Glover said funding changes outlined in the federal budget were so complex that there was insufficient time to implement them by the 2016 start date.

Clive Palmer has renewed threats to block legislation for the higher education agenda, and the ruling bodies for several institutions, including the University of Sydney, are yet to discuss whether to support the proposed changes.

''Our university and others are still trying to understand aspects of the funding package that the government has presented,'' Professor Glover said.

''The decision to remove the cap on fees in 2016 is premature, and I have indicated that in a conversation with the minister's office. I am not the only vice-chancellor who thinks this way.''

School leavers enrolling at university over the next 18 months are particularly exposed to the fee uncertainty. Under the government's plan, these future undergraduates would only be exempt from the new fees for their first year of study. After 2016 they will pay the full new fees for the rest of their course.

As a result universities will need to provide a schedule of the new charges within the next three months before opening up early round offers. Most importantly in NSW, they need to be ready for the 54,000 school students who find out their Australian Tertiary Admission Rank on December 18.

Prime Minister Tony Abbott moved to allay universities concerns on Wednesday, claiming the new fee structures would only apply to students who enrol in courses from 2016 when the changes come into effect.

''If you start a course under one system you'll finish it under that system,'' Mr Abbott told ABC radio.

''If you are studying now your conditions of study won't change. If you start next year your conditions of study won't change. It's only for those who start when these changes kick-in in 2016 that will have the different conditions applying to them.''

Universities Australia chief executive Belinda Robinson urged the government to exercise caution with the implementation of the reform agenda.

''Students planning to go to university in 2015 and beyond will be looking very closely at these reforms,'' Ms Robinson said. ''It's important we get this right because once we go down this path it will be difficult to retrace our steps. We need to … make sure that it is our students whose best interests we are putting ahead of all else.''

Opposition education spokesman Kim Carr said: ''Students entering university in this year's mid-year intake won't know what they will pay at the end of their degrees. Universities are very nervous about these policies and concerns about equity are mounting - even among the Group of 8 universities.''

Professor Peter Booth, the senior deputy vice-chancellor at the University of Technology, Sydney, said the impact of the package needed to be carefully scrutinised.

Charles Sturt University vice-chancellor Andrew Vann said: ''The government has said students who had accepted offers before budget night will not be affected. We are concerned whether our offers for mid-year or for 2015 can stand in the market place.

''We're having to grapple with a lot of detail. The more we look at this, the more questions pop out. There's so much happening at once.''